The UM-BBD Predictive Biodegradation Workshop 4

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Past experience has shown that participation in a pre-workshop exercise greatly facilitates discussion at the workshop. In this context, we have compiled a list of chemical compounds that meet EU Persistent, Bioaccumulative and Toxic (PBT) criteria, for you to run through the UM-BBD Pathway Prediction System (PPS) at

Each of you has been assigned a set of 4-5 compounds from this list, and have been given the SMILES string representation of the compound and its name. Copy and paste each SMILES string, one at a time, into the "Smiles string:" box and click on "Continue."

For each compound, observe the initial prediction, and follow one or more branches for several steps. Print out any web pages that show interesting or problematic predicted transformations, and bring them to the workshop. This part of the exercise should take no more than 20 minutes. Run additional compounds through the system if you want.

For each compound that you have the expertise to do so, rate the overall effectiveness of PPS predictions, using the following effectiveness codes:

  1. excellent
  2. somewhat effective
  3. poor
For each compound you ranked 2 or 3, write a short note on the failings of the system. If any prediction was interesting or insightful, make a note of that too. This rating is OPTIONAL, but please do run the compounds through the system even if you do not give their predicted biotransformations an effectiveness rating.

Evaluate the system:

                      Strongly Agree   Agree      Neutral     Disagree     Strongly Disagree   
a. Easy to use:             1            2           3            4               5
b. Responsive:              1            2           3            4               5
c. Info clearly displayed:  1            2           3            4               5
Please suggest improvements of system format (not its predictions).

New Tools or Methods

If you have developed, or are interested in developing, a tool or method that could improve the PPS, including limiting the combinational explosion of PPS predictions, please write a few sentences on this method, and, if possible, include a reference, reprint or preprint.

Send answers to the above questions, notes and comments, and tools and methods documents (if any), to Lynda Ellis and Larry Wackett by Friday, April 27, 2005. Also, bring a copy to the workshop. We will compile the answers and the compilation will serve as the basis for a part of the workshop discussions.

We appreciate the efforts of the panel members who take the time to work on this project.

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Page Author(s): Larry Wackett and Lynda Ellis

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